TATDN3

TatD DNase domain containing 3

Basic information

Region (hg38): 1:212791827-212816830

Links

ENSG00000203705 ∙ NCBI:128387 ∙ ∙ HGNC:27010 ∙ Uniprot:Q17R31 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TATDN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TATDN3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in TATDN3

This is a list of pathogenic ClinVar variants found in the TATDN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-212791935-G-A		not specified	Uncertain significance (Oct 13, 2021)
1-212797123-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-212797179-A-G		not specified	Uncertain significance (Aug 22, 2022)
1-212802717-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-212802755-A-G		not specified	Uncertain significance (Mar 23, 2022)
1-212804600-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-212804609-C-T		not specified	Uncertain significance (Jul 28, 2021)
1-212804630-A-G		not specified	Uncertain significance (May 23, 2023)
1-212804645-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-212807751-T-C		not specified	Uncertain significance (Nov 19, 2022)
1-212807763-T-C			Likely benign (Jan 01, 2023)
1-212807772-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-212807793-G-A		not specified	Uncertain significance (Jul 16, 2021)
1-212815137-G-A		not specified	Likely benign (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TATDN3	protein_coding	protein_coding	ENST00000532324	10	24799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.44e-7	0.668	125656	1	90	125747	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.432	130	145	0.899	0.00000697	1788
Missense in Polyphen		46	43.888	1.0481		530
Synonymous	0.435	49	53.0	0.924	0.00000242	554
Loss of Function	1.12	12	17.0	0.707	7.25e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00132
Ashkenazi Jewish	0.00	0.00
East Asian	0.000770	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000289	0.000281
Middle Eastern	0.000770	0.000761
South Asian	0.000490	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative deoxyribonuclease.

Intolerance Scores

• loftool: 0.103
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.47

Haploinsufficiency Scores

• pHI: 0.0674
• hipred: N
• hipred_score: 0.174
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.494

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tatdn3
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus
• Molecular function: nuclease activity;metal ion binding